Below you will find a few variations we've implemented for spellcasters, spells, and spellcasting in general for our campaigns. To summarize, the first variation listed below is the Spell Point System that was introduced in Unearthed Arcana, though modified as we found that system had skewed the numbers as it was written. We have also listed a few variants on specific spells found in the core system. Lastly, we've altered the way some of the classes cast and/or access their spells.

Spell Point System
The spell point system presented here allows casters to more freely pick and choose what spells they cast each day. Every spellcaster has a reserve of spell points based on class and level (see the chart below). Characters also gain bonus spell points from a high ability score (just as a normal spellcaster would gain bonus spells from a high ability score). These spell points provide the magical power behind the caster's spells: She spends a number of spell points appropriate to the spell's level to cast the spell. Once spent, spell points are expended until the caster has sufficient time to rest.

With this variant, spellcasters still prepare spells as normal (assuming they normally prepare spells). In effect, casters who prepare spells are setting their list of "spells known" for the day. They need not prepare multiple copies of the same spell, since they can cast any combination of their prepared spells each day (up to the limit of their spell points). Casters still prepare bonus spells of each level as appropriate for high ability scores (if they normally do so). Reference the chart below to see bonus spell slot progression.

Use whichever ability score would normally award bonus spells for the character's class. Then you simply cross-reference the character's relevant ability score with the highest level of spells he can cast, and that number is your amount of bonus points. This value can change each time your ability score undergoes a permanent change (but not from spells or items that boost ability scores, such as Fox's Cunning or a Headband of Intellect) and each time your level changes.

A character who would normally receive bonus spells from a class feature (such as from wizard specialization or access to a Domain) can instead prepare extra spells of the appropriate levels, Domains, and/or Schools. The character doesn't get any extra spell points (and thus can't cast any more spells than normal), but the added flexibility of being able to use the bonus spell more than once per day makes up for that.
For instance, a specialist wizard can prepare one extra spell from the chosen School of each spell level that she can cast. A cleric can prepare one Domain spell of each spell level that he can cast.

For class features that grant bonus spells of a nonfixed spell level (such as the dragon disciple's bonus spells), the character instead gains a number of bonus spell points equal to twice the highest spell level he can cast, minus 1 (minimum 1 point) each time he gains a bonus spell. This is a fixed value--it doesn't increase later as the character gains levels--though later rewards may be larger as appropriate to the character's spellcasting ability.

Characters who cast all their spells spontaneously--such as bards and sorcerers--don't have to prepare spells. They can cast any spell they know by spending the requisite number of spell points.
Characters with the ability to cast a limited number of spells spontaneously (such as druids, who can spontaneously cast a Summon Nature's Ally spell in place of another spell of the same level) are always treated as having those spells prepared, without spending any spell slots to do so. Thus, they can cast such spells any time they have sufficient spell points (in essence these are bonus prepared spells).
Under this system, the Healing Domain becomes a relatively poor choice for good-aligned clerics, since they gain less of a benefit for that Domain.

Figuring out how many spell points that certain prestige classes grant (that do not grant levels that are stackable with another class) is fairly easy. Some are as simple as finding a matching class, such as the Paladin, below. If you cannot find a list that grants exactly the same amount as any below, then use the Cost chart to figure it out the old fashioned way.

Each spell costs a certain number of spell points to cast. The higher the level of the spell, the more points it costs. The chart below covers spells of up to 9th level; increase the costs exponentially for metamagic enhanced spells that would go over this limit.

Spellcasters regain lost spell points whenever they could normally regain spells. Doing this requires the same amount of rest as normal for the class. Spell points are not divorced from the body; they are part of it. Using spell points is mentally tiring, and without the requisite rest period, they do not regenerate.

Utilizing metamagic feats with this system is simple. Effectively, the character must pay for the spell as if it were a higher-level spell, based on the adjustment from the metamagic feat. If the metamagic effect would increase the spell's effective level above what she is normally capable of casting, she can't cast the spell in that way.
Please note that with this system, a character does not need to prepare any spells as metamagic enhanced versions; a caster can simply apply any of the metamagic feats that she knows to a spell (following the restriction mentioned above) at any time. Also note that applying metamagic feats with this system does not increase the casting time, even for spontaneous casters such as sorcerers.

A character with nonstacking spellcasting ability from multiple classes (such as a cleric/wizard) has a separate pool of spell points for each spellcasting class. Such characters may only spend spell points on spells granted by that class. Bonus spell points from a high ability score apply to each pool separately, even if the same ability score is tied to more than one spellcasting class. In the rare situations when a spellcaster has prepared or knows the same spell in two different slots (such as a druid/ranger preparing Delay Poison as both a 2nd level druid spell and a 1st level ranger spell), the character can cast the spell using either pool of spell points, but the spell is treated as being cast by a caster of the level of the class from which the spell points are drawn.

When a character would lose a spell slot (such as from gaining a negative level), he instead loses the number of spell points required to cast his highest-level spell (a spell does not disappear from memory).
Spells that allow a character to recall or recast a spell don't function in this system. (It doesn't make any sense to have a spell that gives you more spell points, since you're either paying more than you get, getting nothing, or getting more than you paid.) Items that function similarly can work, but differently--they restore a number of spell points required to cast a spell of the level. A Pearl of Power for 3rd level spells, for instance, would restore 5 spell points to a character's pool of available points when activated.

Please note that on the table below, spell levels above 9th are listed only for purposes of metamagic enhanced spells.

* NOTE: 0-Level spells cost no points to cast. If a spell caster is capable of casting 0-Level spells, she can cast a number of 0-Level spells equal to three + the number of spell points cast by that class at 1st Level.

One thing about spellcasting that I want noted beyond the spell point system above is the fact that damage caps & bonus caps have been removed for the majority of spells above 2nd level. This means that spells such as Fireball and Lightning Bolt deal 1d6 per caster level, without the maximum of 10d6 (so a 20th level caster would cast a 20d6 Lightning Bolt).
Spells such as those in the Cure Wounds line will not be altered, as they are intentionally set at certain maximums based on level, which I agree with.
Anytime you have a question about a spell, just ask the DM.

As far as spells available for use in the game go, pretty much any spell from any d20 source is a viable option. Exceptions would be when a company makes a spell that is a different version of one already available in the official sourcebooks. More often than not, we'll use the official version. If you have a question about whether or not a spell is allowed, simply ask the DM.

Below you will find a list of official spells that we will be tweaking, mostly because the new version of each leaves a lot to be desired for us old school D&Ders. I liked them more as they were back in previous editions. I may add more to this in future, though I am trying to change as little as possible in order to keep some semblance of game balance in place, and for the sake of simplicity.
We've also found a need to add a higher level version of an existing spell or two (to help fix some of what's wrong with the Epic Level system), which will be included on the list below.
Until such time as we get these spell variations posted on the site, you can see the changes by visiting the appropriate thread on our Forums.

Fire Shield

Protection from Arrows

Stoneskin

Keen Edge

Dispel Magic, Superior (addition)

The other change we've implemented is the way spells are cast by some of the classes. This is in part due to the implementation of the spell-point system, and in part because we've used similar variations in past campaigns across the differing editions. The fact that we simply do not like the Vancian spellcasting system in any way has a lot to do with our decision to make these changes.
Please note that the variations below are in addition to those noted in the Spell Point System information above.

Sorcerers
Mechanically speaking, Sorcerers cast their spells as if they were Spell-like abilities (making them a lot like Psions from the XPH).
Of course, there is one restriction of note to go with that. If a spell has an XP cost, it must still be paid by the sorcerer (this is mainly a game balance issue: could you imagine the abuse one could wreak with the Wish spell if it had no XP cost limitation?).
For sake of ease and game balance, sorcerers are able to apply metamagic feats to their spells as normal, despite the fact that they work like spell-like abilities.

Wizards
A wizard does not have to memorize a new selection of spells each day. Once he has memorized a roster of spells, they stay in memory until such time as he wishes to "swap" one or more out. At any time, under suitable reading conditions, a wizard may opt to release one or more spells from memory, and study a replacement or replacements from his spellbook. Each replacement spell takes 1 minute per spell level to memorize.
Please note that swapping out a spell does not grant further spell points at that time, if any were depleted before studying. You are simply exchanging knowledge of one spell for another. Only normal rest can regenerate your spell point pool.